Viral ancestors of antiviral systems

Viruses

Volumn 3, Issue 10, 2011, Pages 1933-1958

  Villarreal, Luis P ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Adaptive immunity; Addiction modules; Apoptosis; CRISPR; ERV; Evolution of immunity; HERV; Interferon; LTR; MHC; Prophage; Restriction modification; RNAi; T cell receptor; Toxin antitoxin; Virus evolution

Indexed keywords

ALPHA INTERFERON; BACTERIAL TOXIN; GAMMA INTERFERON; IMMUNOGLOBULIN RECEPTOR; PALINDROMIC DNA; T LYMPHOCYTE RECEPTOR;

ADAPTIVE IMMUNITY; CAENORHABDITIS ELEGANS; CELL DIFFERENTIATION; DNA SEQUENCE; ENDOGENOUS RETROVIRUS; ESCHERICHIA COLI; EUKARYOTE EVOLUTION; HABITUAL ADAPTATION; HOST RESISTANCE; MAJOR HISTOCOMPATIBILITY COMPLEX; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE REPEAT; PROKARYOTE; PROPHAGE; RAG1 GENE; RAG2 GENE; RESTRICTION MODIFICATION GENE; REVIEW; RNA INTERFERENCE; TOXIN ANTITOXIN GENE; UROCHORDATA; VIROGENESIS; VIROLOGY; VIRUS CELL TRANSFORMATION; VIRUS GENE; VIRUS IMMUNITY; VIRUS RECOMBINATION;

ADAPTIVE IMMUNITY; ADDICTION MODULES; APOPTOSIS; CRISPR; ERV; EVOLUTION OF IMMUNITY; HERV; INTERFERON; LTR; MHC; PROPHAGE; RESTRICTION MODIFICATION; RNAI; T-CELL RECEPTOR; TOXIN ANTITOXIN; VIRUS EVOLUTION;

ADAPTIVE IMMUNITY; ANIMALS; ANTIVIRAL AGENTS; ARCHAEA; BACTERIA; BIOLOGICAL EVOLUTION; EUKARYOTA; GENE TRANSFER, HORIZONTAL; HUMANS; VIRUSES;

EUKARYOTA; VERTEBRATA;

EID: 80055002160     PISSN: None     EISSN: 19994915     Source Type: Journal    
DOI: 10.3390/v3101933     Document Type: Review

References (212)

1. Breitbart, M.; Hewson, I.; Felts, B.; Mahaffy, J.M.; Nulton, J.; Salamon, P.; Rohwer, F. Metagenomic analyses of an uncultured viral community from human feces. J. Bacteriol. 2003, 185, 6220-6223.
2. Angly, F.E.; Felts, B.; Breitbart, M.; Salamon, P.; Edwards, R.A.; Carlson, C.; Chan, A.M.; Haynes, M.; Kelley, S.; Liu, H.; et al. The marine viromes of four oceanic regions. PLoS Biol. 2006, 4, e368.
3. Santos, F.; Meyerdierks, A.; Pena, A.; Rossello-Mora, R.; Amann, R.; Anton, J. Metagenomic approach to the study of halophages: The environmental halophage 1. Environ. Microbiol. 2007, 9, 1711-1723.
4. Breitbart, M.; Haynes, M.; Kelley, S.; Angly, F.; Edwards, R.A.; Felts, B.; Mahaffy, J.M.; Mueller, J.; Nulton, J.; Rayhawk, S.; et al. Viral diversity and dynamics in an infant gut. Res. Microbiol. 2008, 159, 367-373.
5. Desnues, C.; Rodriguez-Brito, B.; Rayhawk, S.; Kelley, S.; Tran, T.; Haynes, M.; Liu, H.; Furlan, M.; Wegley, L.; Chau, B.; et al. Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature 2008, 452, 340-343.
6. Dinsdale, E.A.; Edwards, R.A.; Hall, D.; Angly, F.; Breitbart, M.; Brulc, J.M.; Furlan, M.; Desnues, C.; Haynes, M.; Li, L.; et al. Functional metagenomic profiling of nine biomes. Nature 2008, 452, 629-632.
7. Schoenfeld, T.; Patterson, M.; Richardson, P.M.; Wommack, K.E.; Young, M.; Mead, D. Assembly of viral metagenomes from yellowstone hot springs. Appl. Environ. Microbiol. 2008, 74, 4164-4174.
8. Williamson, S.J.; Rusch, D.B.; Yooseph, S.; Halpern, A.L.; Heidelberg, K.B.; Glass, J.I.; Andrews-Pfannkoch, C.; Fadrosh, D.; Miller, C.S.; Sutton, G. et al. The sorcerer ii global ocean sampling expedition: Metagenomic characterization of viruses within aquatic microbial samples. PLoS One 2008, 3, e1456.
9. Santos, F.; Yarza, P.; Parro, V.; Briones, C.; Anton, J. The metavirome of a hypersaline environment. Environ. Microbiol. 2010, 12, 2965-2976.
10. Roossinck, M.J.; Saha, P.; Wiley, G.B.; Quan, J.; White, J.D.; Lai, H.; Chavarria, F.; Shen, G.; Roe, B.A. Ecogenomics: Using massively parallel pyrosequencing to understand virus ecology. Mol. Ecol. 2010, 19, 81-88.
11. Witzany, G. Natural genome-editing competences of viruses. Acta Biotheor. 2006, 54, 235-253.
12. Villarreal, L.P.; Witzany, G. Viruses are essential agents within the roots and stem of the tree of life. J. Theor. Biol. 2010, 262, 698-710.
13. Luria, S.E.; Delbruck, M. Mutations of bacteria from virus sensitivity to virus resistance. Genetics 1943, 28, 491-511.
14. d'Herelle, F. The Bacteriophage and Its Behavior; Williams and Wilkins: Baltimore, MD, USA, 1926.
15. Delbrück, M.; Luria, S.E. Interference between bacterial viruses. Arch. Biochem. 1942, I, 111-141.
16. Redfield, R.J.; Campbell, A.M. Origin of cryptic lambda prophages in escherichia coli k-12. Cold Spring Harb. Symp. Quant. Biol. 1984, 49, 199-206.
17. Wain-Hobson, S. Retrovirus evolution. In Origin and Evolution of Viruses, 2nd ed.; Domingo, E., Parrish, C.R., Holland, J.J., Eds.; Academic Press: San Diego, CA, USA, 2008.
18. Villarreal, L.P.; Defilippis, V.R.; Gottlieb, K.A. Acute and persistent viral life strategies and their relationship to emerging diseases. Virology 2000, 272, 1-6.
19. Ryan, F.P. Viruses as symbionts. Symbiosis 2007, 43, 11-21.
20. Roossinck, M.J. The good viruses: Viral mutualistic symbioses. Nat. Rev. Microbiol. 2011, 9, 99-108.
21. Yan, Y.; Buckler-White, A.; Wollenberg, K.; Kozak, C.A. Origin, antiviral function and evidence for positive selection of the gammaretrovirus restriction gene fv1 in the genus mus. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 3259-3263.
22. Mehta, P.; Casjens, S.; Krishnaswamy, S. Analysis of the lambdoid prophage element e14 in the e. Coli k-12 genome. BMC Microbiol. 2004, 4, 4.
23. Engelberg-Kulka, H.; Reches, M.; Narasimhan, S.; Schoulaker-Schwarz, R.; Klemes, Y.; Aizenman, E.; Glaser, G. Rexb of bacteriophage lambda is an anti-cell death gene. Proc. Natl. Acad. Sci. U. S. A. 1998, 95, 15481-15486.
24. Sun, X.M.; Gohler, A.; Heller, K.J.; Neve, H. The ltp gene of temperate streptococcus thermophilus phage tp-j34 confers superinfection exclusion to streptococcus thermophilus and lactococcus lactis. Virology 2006, 350, 146-157.
25. Mosig, G.; Yu, S.; Myung, H.; Haggard-Ljungquist, E.; Davenport, L.; Carlson, K.; Calendar, R. A novel mechanism of virus-virus interactions: Bacteriophage p2 tin protein inhibits phage t4 DNA synthesis by poisoning the t4 single-stranded DNA binding protein, gp32. Virology 1997, 230, 72-81.
26. Hartskeerl, R.; Zuidweg, E.; van Geffen, M.; Hoekstra, W. The inci plasmids r144, r64 and colib belong to one exclusion group. J. Gen. Microbiol. 1985, 131, 1305-1311.
27. Briani, F.; Deho, G.; Forti, F.; Ghisotti, D. The plasmid status of satellite bacteriophage p4. Plasmid 2001, 45, 1-17.
28. Oshima, K.; Kakizawa, S.; Nishigawa, H.; Kuboyama, T.; Miyata, S.; Ugaki, M.; Namba, S. A plasmid of phytoplasma encodes a unique replication protein having both plasmid- and virus-like domains: Clue to viral ancestry or result of virus/plasmid recombination? Virology 2001, 285, 270-277.
29. Boyd, D.; Peters, G.A.; Cloeckaert, A.; Boumedine, K.S.; Chaslus-Dancla, E.; Imberechts, H.; Mulvey, M.R. Complete nucleotide sequence of a 43-kilobase genomic island associated with the multidrug resistance region of salmonella enterica serovar typhimurium dt104 and its identification in phage type dt120 and serovar agona. J. Bacteriol. 2001, 183, 5725-5732.
30. Boltner, D.; MacMahon, C.; Pembroke, J.T.; Strike, P.; Osborn, A.M. R391: A conjugative integrating mosaic comprised of phage, plasmid, and transposon elements. J. Bacteriol. 2002, 184, 5158-5169.
31. Jalasvuori, M.; Jaatinen, S.T.; Laurinavicius, S.; Ahola-Iivarinen, E.; Kalkkinen, N.; Bamford, D.H.; Bamford, J.K.H. The closest relatives of icosahedral viruses of thermophilic bacteria are among viruses and plasmids of the halophilic archaea. J. Virol. 2009, 83, 9388-9397.
32. Lobocka, M.B.; Rose, D.J.; Plunkett, G., 3rd; Rusin, M.; Samojedny, A.; Lehnherr, H.; Yarmolinsky, M.B.; Blattner, F.R. Genome of bacteriophage p1. J. Bacteriol. 2004, 186, 7032-7068.
33. Yarmolinsky, M.B. Programmed cell death in bacterial populations. Science 1995, 267, 836-837.
34. Klassen, R.; Tontsidou, L.; Larsen, M.; Meinhardt, F. Genome organization of the linear cytoplasmic element ppe1b from pichia etchellsii. Yeast 2001, 18, 953-961.
35. Binnewies, T.T.; Motro, Y.; Hallin, P.F.; Lund, O.; Dunn, D.; La, T.; Hampson, D.J.; Bellgard, M.; Wassenaar, T.M.; Ussery, D.W. Ten years of bacterial genome sequencing: Comparativegenomics-based discoveries. Funct. Integr. Genom. 2006, 6, 165-185.
36. Koonin, E.V.; Wolf, Y.I. Genomics of bacteria and archaea: The emerging dynamic view of the prokaryotic world. Nucleic Acids Res. 2008, 36, 6688-6719.
37. Osborn, A.M.; Boltner, D. When phage, plasmids, and transposons collide: Genomic islands, and conjugative- and mobilizable-transposons as a mosaic continuum. Plasmid 2002, 48, 202-212.
38. Lehnherr, H.; Maguin, E.; Jafri, S.; Yarmolinsky, M.B. Plasmid addiction genes of bacteriophage p1: Doc, which causes cell death on curing of prophage, and phd, which prevents host death when prophage is retained. J. Mol. Biol. 1993, 233, 414-428.
39. Basta, T.; Smyth, J.; Forterre, P.; Prangishvili, D.; Peng, X. Novel archaeal plasmid pah1 and its interactions with the lipothrixvirus afv1. Mol. Microbiol. 2009, 71, 23-34.
40. Ichige, A.; Kobayashi, I. Stability of ecori restriction-modification enzymes in vivo differentiates the ecori restriction-modification system from other postsegregational cell killing systems. J. Bacteriol. 2005, 187, 6612-6621.
41. Pagie, L.; Hogeweg, P. Individual- and population-based diversity in restriction-modification systems. Bull. Math. Biol. 2000, 62, 759-774.
42. Gelfand, M.S.; Koonin, E.V. Avoidance of palindromic words in bacterial and archaeal genomes: A close connection with restriction enzymes. Nucleic Acids Res. 1997, 25, 2430-2439.
43. Zhao, F.Q.; Zhang, X.W.; Liang, C.W.; Wu, J.Y.; Bao, Q.Y.; Qin, S. Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria. Physiol. Genom. 2006, 24, 181-190.
44. Dziewit, L.; Jazurek, M.; Drewniak, L.; Baj, J.; Bartosik, D. The sxt conjugative element and linear prophage n15 encode toxin-antitoxin-stabilizing systems homologous to the tad-ata module of the paracoccus aminophilus plasmid pami2. J. Bacteriol. 2007, 189, 1983-1997.
45. Naderer, M.; Brust, J.R.; Knowle, D.; Blumenthal, R.M. Mobility of a restriction-modification system revealed by its genetic contexts in three hosts. J. Bacteriol. 2002, 184, 2411-2419.
46. Tyndall, C.; Lehnherr, H.; Sandmeier, U.; Kulik, E.; Bickle, T.A. The type ic hsd loci of the enterobacteria are flanked by DNA with high homology to the phage p1 genome: Implications for the evolution and spread of DNA restriction systems. Mol. Microbiol. 1997, 23, 729-736.
47. Mrazek, J.; Karlin, S. Detecting alien genes in bacterial genomes. Ann. N. Y. Acad. Sci. 1999, 870, 314-329.
48. Zaleski, P.; Wojciechowski, M.; Piekarowicz, A. The role of dam methylation in phase variation of haemophilus influenzae genes involved in defence against phage infection. Microbiology 2005, 151, 3361-3369.
49. Pullinger, G.D.; Bevir, T.; Lax, A.J. The pasteurella multocida toxin is encoded within a lysogenic bacteriophage. Mol. Microbiol. 2004, 51, 255-269.
50. Persson, O.P.; Pinhassi, J.; Riemann, L.; Marklund, B.I.; Rhen, M.; Normark, S.; Gonzalez, J.M.; Hagstrom, A. High abundance of virulence gene homologues in marine bacteria. Environ. Microbiol. 2009, 11, 1348-1357.
51. Kunin, V.; He, S.; Warnecke, F.; Peterson, S.B.; Garcia Martin, H.; Haynes, M.; Ivanova, N.; Blackall, L.L.; Breitbart, M.; Rohwer, F. et al. A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Res. 2008, 18, 293-297.
52. Williamson, S.J.; Cary, S.C.; Williamson, K.E.; Helton, R.R.; Bench, S.R.; Winget, D.; Wommack, K.E. Lysogenic virus-host interactions predominate at deep-sea diffuse-flow hydrothermal vents. ISME J. 2008, 2, 1112-1121.
53. Rodriguez-Valera, F.; Martin-Cuadrado, A.B.; Rodriguez-Brito, B.; Pasic, L.; Thingstad, T.F.; Rohwer, F.; Mira, A. Explaining microbial population genomics through phage predation. Nat. Rev. Microbiol. 2009, 7, 828-836.
54. Cheetham, B.F.; Katz, M.E. A role for bacteriophages in the evolution and transfer of bacterial virulence determinants. Mol. Microbiol. 1995, 18, 201-208.
55. Ogura, Y.; Ooka, T.; Asadulghani; Terajima, J.; Nougayrede, J.P.; Kurokawa, K.; Tashiro, K.; Tobe, T.; Nakayama, K.; Kuhara, S. et al. Extensive genomic diversity and selective conservation of virulence-determinants in enterohemorrhagic escherichia coli strains of o157 and non-o157 serotypes. Genome Biol. 2007, 8, R138.
56. Ooka, T.; Ogura, Y.; Asadulghani, M.; Ohnishi, M.; Nakayama, K.; Terajima, J.; Watanabe, H.; Hayashi, T. Inference of the impact of insertion sequence (is) elements on bacterial genome diversification through analysis of small-size structural polymorphisms in escherichia coli o157 genomes. Genome Res. 2009, 19, 1809-1816.
57. Zhou, Z.; Li, X.; Liu, B.; Beutin, L.; Xu, J.; Ren, Y.; Feng, L.; Lan, R.; Reeves, P.R.; Wang, L. Derivation of escherichia coli o157:H7 from its o55:H7 precursor. PLoS One 2010, 5, e8700.
58. Ogura, Y.; Ooka, T.; Iguchi, A.; Toh, H.; Asadulghani, M.; Oshima, K.; Kodama, T.; Abe, H.; Nakayama, K.; Kurokawa, K. et al. Comparative genomics reveal the mechanism of the parallel evolution of o157 and non-o157 enterohemorrhagic escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 17939-17944.
59. Iguchi, A.; Thomson, N.R.; Ogura, Y.; Saunders, D.; Ooka, T.; Henderson, I.R.; Harris, D.; Asadulghani, M.; Kurokawa, K.; Dean, P. et al. Complete genome sequence and comparative genome analysis of enteropathogenic escherichia coli o127:H6 strain e2348/69. J. Bacteriol. 2009, 191, 347-354.
60. Asadulghani, M.; Ogura, Y.; Ooka, T.; Itoh, T.; Sawaguchi, A.; Iguchi, A.; Nakayama, K.; Hayashi, T. The defective prophage pool of escherichia coli o157: Prophage-prophage interactions potentiate horizontal transfer of virulence determinants. PLoS Pathog. 2009, 5, e1000408.
61. Abe, H.; Miyahara, A.; Oshima, T.; Tashiro, K.; Ogura, Y.; Kuhara, S.; Ogasawara, N.; Hayashi, T.; Tobe, T. Global regulation by horizontally transferred regulators establishes the pathogenicity of escherichia coli. DNA Res. 2008, 15, 25-38.
62. Oshima, K.; Toh, H.; Ogura, Y.; Sasamoto, H.; Morita, H.; Park, S.H.; Ooka, T.; Iyoda, S.; Taylor, T.D.; Hayashi, T. et al. Complete genome sequence and comparative analysis of the wild-type commensal escherichia coli strain se11 isolated from a healthy adult. DNA Res. 2008, 15, 375-386.
63. Brussow, H. Bacteria between protists and phages: From antipredation strategies to the evolution of pathogenicity. Mol. Microbiol. 2007, 65, 583-589.
64. Kim, Y.; Wang, X.; Ma, Q.; Zhang, X.S.; Wood, T.K. Toxin-antitoxin systems in escherichia coli influence biofilm formation through yjgk (taba) and fimbriae. J. Bacteriol. 2009, 191, 1258-1267.
65. Harrison, J.J.; Wade, W.D.; Akierman, S.; Vacchi-Suzzi, C.; Stremick, C.A.; Turner, R.J.; Ceri, H. The chromosomal toxin gene yafq is a determinant of multidrug tolerance for escherichia coli growing in a biofilm. Antimicrob. Agents Chemother. 2009, 53, 2253-2258.
66. Blower, T.R.; Fineran, P.C.; Johnson, M.J.; Toth, I.K.; Humphreys, D.P.; Salmond, G.P. Mutagenesis and functional characterization of the rna and protein components of the toxin abortive infection and toxin-antitoxin locus of erwinia. J. Bacteriol. 2009, 191, 6029-6039.
67. Fineran, P.C.; Blower, T.R.; Foulds, I.J.; Humphreys, D.P.; Lilley, K.S.; Salmond, G.P. The phage abortive infection system, toxin, functions as a protein-rna toxin-antitoxin pair. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 894-899.
68. Chen, J.; Novick, R.P. Phage-mediated intergeneric transfer of toxin genes. Science 2009, 323, 139-141.
69. Spoering, A.L.; Vulic, M.; Lewis, K. Glpd and plsb participate in persister cell formation in escherichia coli. J. Bacteriol. 2006, 188, 5136-5144.
70. Horvath, P.; Barrangou, R. Crispr/cas, the immune system of bacteria and archaea. Science 2010, 327, 167-170.
71. Marraffini, L.A.; Sontheimer, E.J. Self versus non-self discrimination during crispr rna-directed immunity. Nature 2010, 463, 568-571.
72. Jore, M.M.; Lundgren, M.; van Duijn, E.; Bultema, J.B.; Westra, E.R.; Waghmare, S.P.; Wiedenheft, B.; Pul, U.; Wurm, R.; Wagner, R. et al. Structural basis for crispr rna-guided DNA recognition by cascade. Nat. Struct. Mol. Biol. 2011, 18, 529-536.
73. Marraffini, L.A.; Sontheimer, E.J. Crispr interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 2008, 322, 1843-1845.
74. Horvath, P.; Romero, D.A.; Coute-Monvoisin, A.C.; Richards, M.; Deveau, H.; Moineau, S.; Boyaval, P.; Fremaux, C.; Barrangou, R. Diversity, activity, and evolution of crispr loci in streptococcus thermophilus. J. Bacteriol. 2008, 190, 1401-1412.
75. Snyder, J.C.; Bateson, M.M.; Lavin, M.; Young, M.J. Use of cellular crispr (clusters of regularly interspaced short palindromic repeats) spacer-based microarrays for detection of viruses in environmental samples. Appl. Environ. Microbiol. 2010, 76, 7251-7258.
76. Bize, A.; Forterre, P.; Prangishvili, D. Archeovirus. Virologie 2010, 14, 101-117.
77. Wang, Y.; Duan, Z.H.; Zhu, H.J.; Guo, X.; Wang, Z.Y.; Zhou, J.; She, Q.X.; Huang, L. A novel sulfolobus non-conjugative extrachromosomal genetic element capable of integration into the host genome and spreading in the presence of a fusellovirus. Virology 2007, 363, 124-133.
78. Zegans, M.E.; Wagner, J.C.; Cady, K.C.; Murphy, D.M.; Hammond, J.H.; O'Toole, G.A. Interaction between bacteriophage dms3 and host crispr region inhibits group behaviors of pseudomonas aeruginosa. J. Bacteriol. 2009, 191, 210-219.
79. Shah, S.A.; Hansen, N.R.; Garrett, R.A. Distribution of crispr spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism. Biochem. Soc. Trans. 2009, 37, 23-28.
80. Touchon, M.; Rocha, E.P.C. The small, slow and specialized crispr and anti-crispr of Escherichia and salmonella. PLoS One 2010, 5, e11126.
81. Gill, E.E.; Brinkman, F.S.L. The proportional lack of archaeal pathogens: Do viruses/phages hold the key? Bioessays 2011, 33, 248-254.
82. Agarkova, I.V.; Dunigan, D.D.; Van Etten, J.L. Virion-associated restriction endonucleases of chloroviruses. J. Virol. 2006, 80, 8114-8123.
83. Volff, J.N.; Korting, C.; Froschauer, A.; Sweeney, K.; Schartl, M. Non-ltr retrotransposons encoding a restriction enzyme-like endonuclease in vertebrates. J. Mol. Evol. 2001, 52, 351-360.
84. Fire, A.; Xu, S.; Montgomery, M.K.; Kostas, S.A.; Driver, S.E.; Mello, C.C. Potent and specific genetic interference by double-stranded RNA in caenorhabditis elegans. Nature 1998, 391, 806-811.
85. Tomari, Y.; Zamore, P.D. Perspective: Machines for RNAi. Gene. Dev. 2005, 19, 517-529.
86. Anglicheau, D.; Muthukumar, T.; Suthanthiran, M. Micrornas: Small rnas with big effects. Transplantation 2010, 90, 105-112.
87. Lu, R.; Yigit, E.; Li, W.X.; Ding, S.W. An rig-i-like rna helicase mediates antiviral rnai downstream of viral sirna biogenesis in caenorhabditis elegans. PLoS Pathog. 2009, 5, e1000286.
88. Sijen, T.; Fleenor, J.; Simmer, F.; Thijssen, K.L.; Parrish, S.; Timmons, L.; Plasterk, R.H.; Fire, A. On the role of rna amplification in dsrna-triggered gene silencing. Cell 2001, 107, 465-476.
89. Iyer, L.M.; Koonin, E.V.; Aravind, L. Evolutionary connection between the catalytic subunits of DNA-dependent rna polymerases and eukaryotic rna-dependent rna polymerases and the origin of rna polymerases. BMC Struct. Biol. 2003, 3, 1.
90. Jin, L.; Kryukov, K.; Suzuki, Y.; Imanishi, T.; Ikeo, K.; Gojobori, T. The evolutionary study of small rna-directed gene silencing pathways by investigating rnase iii enzymes. Gene 2009, 435, 1-8.
91. Barstead, R. Genome-wide rnai. Curr. Opin. Chem. Biol. 2001, 5, 63-66.
92. van Roessel, P.; Brand, A.H. Spreading silence with sid. Genome Biol. 2004, 5, 208.
93. May, R.C.; Plasterk, R.H. Rna interference spreading in c. Elegans. Meth. Enzymol. 2005, 392, 308-315.
94. Felix, M.A.; Ashe, A.; Piffaretti, J.; Wu, G.; Nuez, I.; Belicard, T.; Jiang, Y.; Zhao, G.; Franz, C.J.; Goldstein, L.D. et al. Natural and experimental infection of caenorhabditis nematodes by novel viruses related to nodaviruses. PLoS Biol. 2011, 9, e1000586.
95. Bekal, S.; Domier, L.; Niblack, T.; Lambert, K. Discovery and initial analysis of novel viral genomes in the soybean cyst nematode. J. Gen. Virol. 2011, 92, 1870-1879.
96. Bagasra, O.; Prilliman, K.R. Rna interference: The molecular immune system. J. Mol. Histol. 2004, 35, 545-553.
97. Lu, R.; Maduro, M.; Li, F.; Li, H.W.; Broitman-Maduro, G.; Li, W.X.; Ding, S.W. Animal virus replication and rnai-mediated antiviral silencing in caenorhabditis elegans. Nature 2005, 436, 1040-1043.
98. Schott, D.H.; Cureton, D.K.; Whelan, S.P.; Hunter, C.P. An antiviral role for the rna interference machinery in caenorhabditis elegans. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 18420-18424.
99. Wilkins, C.; Dishongh, R.; Moore, S.C.; Whitt, M.A.; Chow, M.; Machaca, K. Rna interference is an antiviral defence mechanism in caenorhabditis elegans. Nature 2005, 436, 1044-1047.
100. Fritz, J.H.; Girardin, S.E.; Philpott, D.J. Innate immune defense through RNA interference. Sci. STKE 2006, 2006, pe27.
101. Bowen, N.J.; McDonald, J.F. Genomic analysis of caenorhabditis elegans reveals ancient families of retroviral-like elements. Genome Res. 1999, 9, 924-935.
102. Vastenhouw, N.L.; Plasterk, R.H. Rnai protects the caenorhabditis elegans germline against transposition. Trends Genet 2004, 20, 314-319.
103. Robert, V.J.; Sijen, T.; van Wolfswinkel, J.; Plasterk, R.H. Chromatin and rnai factors protect the c. Elegans germline against repetitive sequences. Gene. Dev. 2005, 19, 782-787.
104. Villarreal, L.P. Origin of Group Identity: Viruses, Addiction, and Cooperation; Springer: New York, NY, USA, 2009; pp. xxiv, 614, 619, plates.
105. Voinnet, O. Induction and suppression of rna silencing: Insights from viral infections.Nat. Rev. 2005, 6, 206-220.
106. Malone, C.D.; Hannon, G.J. Small rnas as guardians of the genome. Cell 2009, 136, 656-668.
107. Wu, Q.; Luo, Y.; Lu, R.; Lau, N.; Lai, E.C.; Li, W.X.; Ding, S.W. Virus discovery by deep sequencing and assembly of virus-derived small silencing rnas. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 1606-1611.
108. Pelisson, A.; Sarot, E.; Payen-Groschene, G.; Bucheton, A. A novel repeat-associated small interfering rna-mediated silencing pathway downregulates complementary sense gypsy transcripts in somatic cells of the drosophila ovary. J. Virol. 2007, 81, 1951-1960.
109. Czech, B.; Malone, C.D.; Zhou, R.; Stark, A.; Schlingeheyde, C.; Dus, M.; Perrimon, N.; Kellis, M.; Wohlschlegel, J.A.; Sachidanandam, R. et al. An endogenous small interfering rna pathway in drosophila. Nature 2008, 453, U798-U797.
110. Aravind, L.; Dixit, V.M.; Koonin, E.V. Apoptotic molecular machinery: Vastly increased complexity in vertebrates revealed by genome comparisons. Science 2001, 291, 1279-1284.
111. Nakayashiki, H.; Kadotani, N.; Mayama, S. Evolution and diversification of rna silencing proteins in fungi. J. Mol. Evol. 2006, 63, 127-135.
112. de Jong, D.; Eitel, M.; Jakob, W.; Osigus, H.J.; Hadrys, H.; Desalle, R.; Schierwater, B. Multiple dicer genes in the early-diverging metazoa. Mol. Biol. Evol. 2009, 26, 1333-1340.
113. Ghabrial, S.A. New developments in fungal virology. Adv. Virus Res. 1994, 43, 303-388.
114. Hillman, B.I.; Supyani, S.; Kondo, H.; Suzuki, N. A reovirus of the fungus cryphonectria parasitica that is infectious as particles and related to the coltivirus genus of animal pathogens. J. Virol. 2004, 78, 892-898.
115. Pearson, M.N.; Beever, R.E.; Boine, B.; Arthur, K. Mycoviruses of filamentous fungi and their relevance to plant pathology. Mol. Plant Pathol. 2009, 10, 115-128.
116. Ghabrial, S.A. Origin, adaptation and evolutionary pathways of fungal viruses. Virus Genes 1998, 16, 119-131.
117. Biella, S.; Smith, M.L.; Aist, J.R.; Cortesi, P.; Milgroom, M.G. Programmed cell death correlates with virus transmission in a filamentous fungus. Proc. Roy. Soc. Lond. B Biol. Sci. 2002, 269, 2269-2276.
118. Allen, T.D.; Nuss, D.L. Linkage between mitochondrial hypovirulence and viral hypovirulence in the chestnut blight fungus revealed by cdna microarray analysis. Eukaryotic. Cell 2004, 3, 1227-1232.
119. Cortesi, P.; McCulloch, C.E.; Song, H.Y.; Lin, H.Q.; Milgroom, M.G. Genetic control of horizontal virus transmission in the chestnut blight fungus, cryphonectria parasitica. Genetics 2001, 159, 107-118.
120. Liu, Y.C.; Linder-Basso, D.; Hillman, B.I.; Kaneko, S.; Milgroom, M.G. Evidence for interspecies transmission of viruses in natural populations of filamentous fungi in the genus cryphonectria. Mol. Ecol. 2003, 12, 1619-1628.
121. Liu, H.; Fu, Y.; Jiang, D.; Li, G.; Xie, J.; Cheng, J.; Peng, Y.; Ghabrial, S.A.; Yi, X. idespread horizontal gene transfer from double-stranded rna viruses to eukaryotic nuclear genomes. J. Virol. 2010, 84, 11876-11887.
122. Hammond, T.M.; Bok, J.W.; Andrewski, M.D.; Reyes-Dominguez, Y.; Scazzocchio, C.; Keller, N.P. Rna silencing gene truncation in the filamentous fungus aspergillus nidulans. Eukaryot. Cell 2008, 7, 339-349.
123. Hammond, T.M.; Keller, N.P. Rna silencing in aspergillus nidulans is independent of RNA-dependent RNA polymerases. Genetics 2005, 169, 607-617.
124. Cogoni, C. Homology-dependent gene silencing mechanisms in fungi. Annu. Rev. Microbiol. 2001, 55, 381-406.
125. Daboussi, M.J.; Capy, P. Transposable elements in filamentous fungi. Annu. Rev. Microbiol. 2003, 57, 275-299.
126. Ebbole, D.J. Magnaporthe as a model for understanding host-pathogen interactions. Annu. Rev. Phytopathology 2007, 45, 437-456.
127. Gorinsek, B.; Gubensek, F.; Kordis, D. Phylogenomic analysis of chromoviruses. Cytogenet. Genome Res. 2005, 110, 543-552.
128. Delsuc, F.; Brinkmann, H.; Chourrout, D.; Philippe, H. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 2006, 439, 965-968.
129. Klein, J. The grapes of incompatibility. Dev. Cell 2006, 10, 2-4.
130. Oren, M.; Douek, J.; Fishelson, Z.; Rinkevich, B. Identification of immune-relevant genes in histoincompatible rejecting colonies of the tunicate botryllus schlosseri. Dev. Comp. Immunol. 2007, 31, 889-902.
131. Pancer, Z.; Saha, N.R.; Kasamatsu, J.; Suzuki, T.; Amemiya, C.T.; Kasahara, M.; Cooper, M.D. Variable lymphocyte receptors in hagfish. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 9224-9229.
132. Rogozin, I.B.; Iyer, L.M.; Liang, L.; Glazko, G.V.; Liston, V.G.; Pavlov, Y.I.; Aravind, L.; Pancer, Z. Evolution and diversification of lamprey antigen receptors: Evidence for involvement of an aid-apobec family cytosine deaminase. Nat. Immunol. 2007, 8, 647-656.
133. Nonaka, M.; Yoshizaki, F. Primitive complement system of invertebrates. Immunol. Rev. 2004, 198, 203-215.
134. Marino, R.; Kimura, Y.; De Santis, R.; Lambris, J.D.; Pinto, M.R. Complement in urochordates: Cloning and characterization of two c3-like genes in the ascidian ciona intestinalis. Immunogenetics 2002, 53, 1055-1064.
135. Mansour, M.H.; Cooper, E.L. Tunicate thy-1-An invertebrate member of the ig superfamily. Progr. Clin. Biol. Res. 1987, 233, 33-42.
136. Herrin, B.R.; Cooper, M.D. Alternative adaptive immunity in jawless vertebrates. J. Immunol. 2010, 185, 1367-1374.
137. Hsu, E. The invention of lymphocytes. Curr. Opin. Immunol. 2010, 23, 156-162.
138. Britten, R.J.; McCormack, T.J.; Mears, T.L.; Davidson, E.H. Gypsy/ty3-class retrotransposons integrated in the DNA of herring, tunicate, and echinoderms. J. Mol. Evol. 1995, 40, 13-24.
139. Volff, J.N.; Lehrach, H.; Reinhardt, R.; Chourrout, D. Retroelement dynamics and a novel type of chordate retrovirus-like element in the miniature genome of the tunicate oikopleura dioica. Mol. Biol. Evol. 2004, 21, 2022-2033.
140. Dehal, P.; Satou, Y.; Campbell, R.K.; Chapman, J.; Degnan, B.; De Tomaso, A.; Davidson, B.; Di Gregorio, A.; Gelpke, M.; Goodstein, D.M. et al. The draft genome of ciona intestinalis: Insights into chordate and vertebrate origins. Science 2002, 298, 2157-2167.
141. Gadd, T.; Jakava-Viljanen, M.; Tapiovaara, H.; Koski, P.; Sihvonen, L. Epidemiological aspects of viral haemorrhagic septicaemia virus genotype ii isolated from baltic herring, clupea harengus membras l. J. Fish Dis. 2011, 34, 517-529.
142. Liongue, C.; John, L.B.; Ward, A. Origins of adaptive immunity. Crit. Rev. Immunol. 2011, 31, 61-71.
143. Litman, G.W.; Rast, J.P.; Fugmann, S.D. The origins of vertebrate adaptive immunity. Nat. Rev. Immunol. 2010, 10, 543-553.
144. Witzany, G. Natural genome editing from a biocommunicative perspective. Biosemiotics 2011, doi:10.1007/s12304-011-9111-7.
145. Shapiro, J.A. Evolution: A View from the 21st Century; FT Press Science: Upper Saddle River, NJ, USA, 2011; pp. xi, 253.
146. Witzany, G. The agents of natural genome editing. J. Mol. Cell Biol. 2011, 3, 181-189.
147. Cooper, M.D.; Alder, M.N. The evolution of adaptive immune systems. Cell 2006, 124, 815-822.
148. Villarreal, L.P. The source of self: Genetic parasites and the origin of adaptive immunity. Ann. N. Y. Acad. Sci. 2009, 1178, 194-232.
149. Jaillon, O.; Aury, J.M.; Brunet, F.; Petit, J.L.; Stange-Thomann, N.; Mauceli, E.; Bouneau, L.; Fischer, C.; Ozouf-Costaz, C.; Bernot, A. et al. Genome duplication in the teleost fish tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 2004, 431, 946-957.
150. Poulter, R.; Butler, M. A retrotransposon family from the pufferfish (fugu) fugu rubripes. Gene 1998, 215, 241-249.
151. Gorinsek, B.; Gubensek, F.; Kordis, D. Evolutionary genomics of chromoviruses in eukaryotes. Mol. Biol. Evol. 2004, 21, 781-798.
152. Mulero, V.; Lopez-Munoz, A.; Roca, F.J.; Meseguer, J. New insights into the evolution of ifns: Zebrafish group ii ifns induce a rapid and transient expression of ifn-dependent genes and display powerful antiviral activities. J. Immunol. 2009, 182, 3440-3449.
153. Workenhe, S.T.; Rise, M.L.; Kibenge, M.J.; Kibenge, F.S. The fight between the teleost fish immune response and aquatic viruses. Mol. Immunol. 2010, 47, 2525-2536.
154. Muroga, K. Viral and bacterial diseases of marine fish and shellfish in japanese hatcheries. Aquaculture 2001, 202, 23-44.
155. Magnadottir, B. Immunological control of fish diseases. Mar. Biotechnol. 2010, 12, 361-379.
156. Matsunaga, T.; Rahman, A. What brought the adaptive immune system to vertebrates?-The jaw hypothesis and the seahorse. Immunol. Rev. 1998, 166, 177-186.
157. L. Speculations on the origin of the vertebrate immune system. Immunol. Lett. 2004, 92, 3-9.
158. Makino, T.; McLysaght, A. Interacting gene clusters and the evolution of the vertebrate immune system. Mol. Biol. Evol. 2008, 25, 1855-1862.
159. Du Pasquier, L. Innate immunity in early chordates and the appearance of adaptive immunity. Comptes Rendus Biologies 2004, 327, 591-601.
160. Dermody, T.S.; Kirchner, E.; Guglielmi, K.M.; Stehle, T. Immunoglobulin superfamily virus receptors and the evolution of adaptive immunity. PLoS Pathog. 2009, 5, e1000481.
161. Carson, S.D. Coxsackievirus and adenovirus receptor (car) is modified and shed in membrane vesicles. Biochemistry 2004, 43, 8136-8142.
162. Adelman, M.K.; Schluter, S.F.; Marchalonis, J.J. The natural antibody repertoire of sharks and humans recognizes the potential universe of antigens. Protein J. 2004, 23, 103-118.
163. Camargo, M.M.; Nahum, L.A. Adapting to a changing world: Rag genomics and evolution. Hum. Genom. 2005, 2, 132-137.
164. Agrawal, A.; Eastman, Q.M.; Schatz, D.G. Transposition mediated by rag1 and rag2 and its implications for the evolution of the immune system. Nature 1998, 394, 744-751.
165. Hiom, K.; Melek, M.; Gellert, M. DNA transposition by the rag1 and rag2 proteins: A possible source of oncogenic translocations. Cell 1998, 94, 463-470.
166. Fugmann, S.D. The origins of the rag genes-from transposition to v(d)j recombination. Semin. Immunol. 2010, 22, 10-16.
167. Hashimoto, K.; Okamura, K.; Yamaguchi, H.; Ototake, M.; Nakanishi, T.; Kurosawa, Y. Conservation and diversification of mhc class i and its related molecules in vertebrates. Immunol. Rev. 1999, 167, 81-100.
168. Xie, T.; Rowen, L.; Aguado, B.; Ahearn, M.E.; Madan, A.; Qin, S.; Campbell, R.D.; Hood, L. Analysis of the gene-dense major histocompatibility complex class iii region and its comparison to mouse. Genome Res. 2003, 13, 2621-2636.
169. Deakin, J.E.; Papenfuss, A.T.; Belov, K.; Cross, J.G.; Coggill, P.; Palmer, S.; Sims, S.; Speed, T.P.; Beck, S.; Graves, J.A. Evolution and comparative analysis of the mhc class iii inflammatory region. BMC Genom. 2006, 7, 281.
170. Andersson, G.; Svensson, A.C.; Setterblad, N.; Rask, L. Retroelements in the human mhc class ii region. Trends Genet. 1998, 14, 109-114.
171. Kulski, J.K.; Gaudieri, S.; Inoko, H.; Dawkins, R.L. Comparison between two human endogenous retrovirus (herv)-rich regions within the major histocompatibility complex. J. Mol. Evol. 1999, 48, 675-683.
172. Matsuo, M.Y.; Nonaka, M. Repetitive elements in the major histocompatibility complex (mhc) class i region of a teleost, medaka: Identification of novel transposable elements. Mech. Dev. 2004, 121, 771-777.
173. Gaudieri, S.; Kulski, J.K.; Balmer, L.; Giles, K.M.; Inoko, H.; Dawkins, R.L. Retroelements and segmental duplications in the generation of diversity within the mhc. DNA Seq. 1997, 8, 137-141.
174. Kulski, J.K.; Shiina, T.; Anzai, T.; Kohara, S.; Inoko, H. Comparative genomic analysis of the mhc: The evolution of class i duplication blocks, diversity and complexity from shark to man. Immunol. Rev. 2002, 190, 95-122.
175. Kulski, J.K.; Anzai, T.; Inoko, H. Ervk9, transposons and the evolution of mhc class i duplicons within the alpha-block of the human and chimpanzee. Cytogenet Genome Res. 2005, 110, 181-192.
176. Kulski, J.K.; Gaudieri, S.; Martin, A.; Dawkins, R.L. Coevolution of perb11 (mic) and hla class I genes with herv-16 and retroelements by extended genomic duplication. J. Mol. Evol. 1999, 49, 84-97.
177. Kulski, J.K.; Gaudieri, S.; Dawkins, R.L. Using alu j elements as molecular clocks to trace the evolutionary relationships between duplicated hla class i genomic segments. J. Mol. Evol. 2000, 50, 510-519.
178. Kulski, J.K.; Anzai, T.; Shiina, T.; Inoko, H. Rhesus macaque class i duplicon structures, organization, and evolution within the alpha block of the major histocompatibility complex. Mol. Biol. Evol. 2004, 21, 2079-2091.
179. Doxiadis, G.G.; de Groot, N.; Bontrop, R.E. Impact of endogenous intronic retroviruses on major histocompatibility complex class II diversity and stability. J. Virol. 2008, 82, 6667-6677.
180. Kulski, J.K.; Dawkins, R.L. The p5 multicopy gene family in the mhc is related in sequence to human endogenous retroviruses HERV-L and HERV-16. Immunogenetics 1999, 49, 404-412.
181. Magor, B.G.; Magor, K.E. Evolution of effectors and receptors of innate immunity. Dev. Comp. Immunol. 2001, 25, 651-682.
182. Nehyba, J.; Hrdlickova, R.; Bose, H.R. Dynamic evolution of immune system regulators: The history of the interferon regulatory factor family. Mol. Biol. Evol. 2009, 26, 2539-2550.
183. Fox, B.A.; Sheppard, P.O.; O'Hara, P.J. The role of genomic data in the discovery, annotation and evolutionary interpretation of the interferon-lambda family. PLoS One 2009, 4, e4933.
184. Robalino, J.; Bartlett, T.C.; Chapman, R.W.; Gross, P.S.; Browdy, C.L.; Warr, G.W. Doublestranded rna and antiviral immunity in marine shrimp: Inducible host mechanisms and evidence for the evolution of viral counter-responses. Dev. Comp. Immunol. 2007, 31, 539-547.
185. Tanaka-Taya, K.; Sashihara, J.; Kurahashi, H.; Amo, K.; Miyagawa, H.; Kondo, K.; Okada, S.; Yamanishi, K. Human herpesvirus 6 (hhv-6) is transmitted from parent to child in an integrated form and characterization of cases with chromosomally integrated hhv-6 DNA. J. Med. Virol. 2004, 73, 465-473.
186. Takemoto, M.; Imasawa, T.; Yamanishi, K.; Mori, Y. Role of dendritic cells infected with human herpesvirus 6 in virus transmission to cd4(+) t cells. Virology 2009, 385, 294-302.
187. 8+ t cells is critical for superinfection by cytomegalovirus. Science 2010, 328, 102-106.
188. Klenerman, P.; Dunbar, P.R. Cmv and the art of memory maintenance. Immunity 2008, 29, 520-522.
189. Lestou, V.S.; De Braekeleer, M.; Strehl, S.; Ott, G.; Gadner, H.; Ambros, P.F. Non-random integration of epstein-barr virus in lymphoblastoid cell lines. Gene. Chromosome. Canc. 1993, 8, 38-48.
190. Hengel, H.; Koszinowski, U.H.; Conzelmann, K.K. Viruses know it all: New insights into ifn networks. Trends Immunol. 2005, 26, 396-401.
191. Vossen, M.T.; Westerhout, E.M.; Soderberg-Naucler, C.; Wiertz, E.J. Viral immune evasion: A masterpiece of evolution. Immunogenetics 2002, 54, 527-542.
192. McGeoch, D.J.; Rixon, F.J.; Davison, A.J. Topics in herpesvirus genomics and evolution. Virus Res. 2006, 117, 90-104.
193. van Cleef, K.W.; Smit, M.J.; Bruggeman, C.A.; Vink, C. Cytomegalovirus-encoded homologs of g protein-coupled receptors and chemokines. J. Clin. Virol. 2006, 35, 343-348.
194. Davis-Poynter, N.J.; Degli-Esposti, M.; Farrell, H.E. Murine cytomegalovirus homologues of cellular immunomodulatory genes. Intervirology 1999, 42, 331-341.
195. Miller-Kittrell, M.; Sparer, T.E. Feeling manipulated: Cytomegalovirus immune manipulation. Virol. J. 2009, 6, 4.
196. Pinto, A.K.; Munks, M.W.; Koszinowski, U.H.; Hill, A.B. Coordinated function of murine cytomegalovirus genes completely inhibits ctl lysis. J. Immunol. 2006, 177, 3225-3234.
197. Brunovskis, P.; Kung, H.J. Retrotransposition and herpesvirus evolution. Virus Genes 1995, 11,259-270.
198. Becker, Y.; Asher, Y.; Bujanover, S.; Darai, G. The dynamic herpesvirus DNA genome: The case of mdv-1 and hsv-1. Acta Virologica 1999, 43, 81-89.
199. Klein, J. Did viruses play a part in the origin of the adaptive immune system? Folia Biologica 2004, 50, 87-92.
200. Hunter, P. The great leap forward. Major evolutionary jumps might be caused by changes in gene regulation rather than the emergence of new genes. EMBO Rep. 2008, 9, 608-611.
201. Zuckerkandl, E.; Cavalli, G. Combinatorial epigenetics, junk DNA, and the evolution of complex organisms. Gene 2007, 390, 232-242.
202. Khodosevich, K.; Lebedev, Y.; Sverdlov, E. Endogenous retroviruses and human evolution. Comp. Funct. Genom. 2002, 3, 494-498.
203. Haygood, R.; Babbitt, C.C.; Fedrigo, O.; Wray, G.A. Contrasts between adaptive coding and noncoding changes during human evolution. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 7853-7857.
204. Buzdin, A.A. Functional analysis of retroviral endogenous inserts in the human genome evolution. Bioorganicheskaia Khimiia 2010, 36, 38-46.
205. Gogvadze, E.; Stukacheva, E.; Buzdin, A.; Sverdlov, E. Human-specific modulation of transcriptional activity provided by endogenous retroviral insertions. J. Virol. 2009, 83, 6098-6105.
206. Cohen, C.J.; Lock, W.M.; Mager, D.L. Endogenous retroviral ltrs as promoters for human genes: A critical assessment. Gene 2009, 448, 105-114.
207. Buzdin, A. Human-specific endogenous retroviruses. Sci. World J. 2007, 7, 1848-1868.
208. Jordan, I.K.; Rogozin, I.B.; Glazko, G.V.; Koonin, E.V. Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet. 2003, 19, 68-72.
209. Oja, M.; Peltonen, J.; Blomberg, J.; Kaski, S. Methods for estimating human endogenous retrovirus activities from est databases. BMC Bioinformatics 2007, 8, S11.
210. Keightley, P.D.; Lercher, M.J.; Eyre-Walker, A. Evidence for widespread degradation of gene control regions in hominid genomes. PLoS Biol. 2005, 3, e42.
211. Anzai, T.; Shiina, T.; Kimura, N.; Yanagiya, K.; Kohara, S.; Shigenari, A.; Yamagata, T.; Kulski, J.K.; Naruse, T.K.; Fujimori, Y. et al. Comparative sequencing of human and chimpanzee mhc class i regions unveils insertions/deletions as the major path to genomic divergence. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 7708-7713.
212. Steinhuber, S.; Brack, M.; Hunsmann, G.; Schwelberger, H.; Dierich, M.P.; Vogetseder, W. Distribution of human endogenous retrovirus herv-k genomes in humans and different primates. Hum. Genet. 1995, 96, 188-192.